Metabarcoding of the phytotelmata of Pseudalcantarea grandis (Bromeliaceae) from an arid zone
Background Pseudalcantarea grandis (Schltdl.) Pinzón & Barfuss is a tank bromeliad that grows on cliffs in the southernmost portion of the Chihuahuan desert. Phytotelmata are water bodies formed by plants that function as micro-ecosystems where bacteria, algae, protists, insects, fungi, and some vertebrates can develop. We hypothesized that the bacterial diversity contained in the phytotelma formed in a bromeliad from an arid zone would differ in sites with and without surrounding vegetation. Our study aimed to characterize the bacterial composition and putative metabolic functions in P. grandis phytotelmata collected in vegetated and non-vegetated sites. Methods Water from 10 individuals was sampled. Five individuals had abundant surrounding vegetation, and five had little or no vegetation. We extracted DNA and amplified seven hypervariable regions of the 16S gene (V2, V4, V8, V3–6, 7–9). Metabarcoding sequencing was performed on the Ion Torrent PGM platform. Taxonomic identity was assigned by the binning reads and coverage between hit and query from the reference database of at least 90%. Putative metabolic functions of the bacterial families were assigned mainly using the FAPROTAX database. The dominance patterns in each site were visualized with rank/abundance curves using the number of Operational Taxonomic Units (OTUs) per family. A percentage similarity analysis (SIMPER) was used to estimate dissimilarity between the sites. Relationships among bacterial families (identified by the dominance analysis and SIMPER), sites, and their respective putative functions were analyzed with shade plots. Results A total of 1.5 million useful bacterial sequences were obtained. Sequences were clustered into OTUs, and taxonomic assignment was conducted using BLAST in the Greengenes databases. Bacterial diversity was 23 phyla, 52 classes, 98 orders, 218 families, and 297 genera. Proteobacteria (37%), Actinobacteria (19%), and Firmicutes (15%) comprised the highest percentage (71%). There was a 68.3% similarity between the two sites at family level, with 149 families shared. Aerobic chemoheterotrophy and fermentation were the main metabolic functions in both sites, followed by ureolysis, nitrate reduction, aromatic compound degradation, and nitrogen fixation. The dominant bacteria shared most of the metabolic functions between sites. Some functions were recorded for one site only and were related to families with the lowest OTUs richness. Bacterial diversity in the P. grandis tanks included dominant phyla and families present at low percentage that could be considered part of a rare biosphere. A rare biosphere can form genetic reservoirs, the local abundance of which depends on external abiotic and biotic factors, while their interactions could favor micro-ecosystem resilience and resistance.
Herrera-García et al. (2022) Metabarcoding of the phytotelmata of Pseudalcantarea grandis (Bromeliaceae) from an arid zone. PeerJ 10:e12706 https://doi.org/10.7717/peerj.12706
Beyond RuBisCO: convergent molecular evolution of multiple chloroplast genes in C4 plants
Background The recurrent evolution of the C4 photosynthetic pathway in angiosperms represents one of the most extraordinary examples of convergent evolution of a complex trait. Comparative genomic analyses have unveiled some of the molecular changes associated with the C4 pathway. For instance, several key enzymes involved in the transition from C3 to C4 photosynthesis have been found to share convergent amino acid replacements along C4 lineages. However, the extent of convergent replacements potentially associated with the emergence of C4 plants remains to be fully assessed. Here, we conducted an organelle-wide analysis to determine if convergent evolution occurred in multiple chloroplast proteins beside the well-known case of the large RuBisCO subunit encoded by the chloroplast gene rbcL. Methods Our study was based on the comparative analysis of 43 C4 and 21 C3 grass species belonging to the PACMAD clade, a focal taxonomic group in many investigations of C4 evolution. We first used protein sequences of 67 orthologous chloroplast genes to build an accurate phylogeny of these species. Then, we inferred amino acid replacements along 13 C4 lineages and 9 C3 lineages using reconstructed protein sequences of their reference branches, corresponding to the branches containing the most recent common ancestors of C4-only clades and C3-only clades. Pairwise comparisons between reference branches allowed us to identify both convergent and non-convergent amino acid replacements between C4:C4, C3:C3 and C3:C4 lineages. Results The reconstructed phylogenetic tree of 64 PACMAD grasses was characterized by strong supports in all nodes used for analyses of convergence. We identified 217 convergent replacements and 201 non-convergent replacements in 45/67 chloroplast proteins in both C4 and C3 reference branches. C4:C4 branches showed higher levels of convergent replacements than C3:C3 and C3:C4 branches. Furthermore, we found that more proteins shared unique convergent replacements in C4 lineages, with both RbcL and RpoC1 (the RNA polymerase beta’ subunit 1) showing a significantly higher convergent/non-convergent replacements ratio in C4 branches. Notably, more C4:C4 reference branches showed higher numbers of convergent vs. non-convergent replacements than C3:C3 and C3:C4 branches. Our results suggest that, in the PACMAD clade, C4 grasses experienced higher levels of molecular convergence than C3 species across multiple chloroplast genes. These findings have important implications for our understanding of the evolution of the C4 photosynthesis pathway.
Casola et al. (2022) Beyond RuBisCO: convergent molecular evolution of multiple chloroplast genes in C4 plants. PeerJ 10:e12791 https://doi.org/10.7717/peerj.12791
Soil health and nutrient density: preliminary comparison of regenerative and conventional farming
Several independent comparisons indicate regenerative farming practices enhance the nutritional profiles of crops and livestock. Measurements from paired farms across the United States indicate differences in soil health and crop nutrient density between fields worked with conventional (synthetically-fertilized and herbicide-treated) or regenerative practices for 5 to 10 years. Specifically, regenerative farms that combined no-till, cover crops, and diverse rotations—a system known as Conservation Agriculture—produced crops with higher soil organic matter levels, soil health scores, and levels of certain vitamins, minerals, and phytochemicals. In addition, crops from two regenerative no-till vegetable farms, one in California and the other in Connecticut, had higher levels of phytochemicals than values reported previously from New York supermarkets. Moreover, a comparison of wheat from adjacent regenerative and conventional no-till fields in northern Oregon found a higher density of mineral micronutrients in the regenerative crop. Finally, a comparison of the unsaturated fatty acid profile of beef and pork raised on one of the regenerative farms to a regional health-promoting brand and conventional meat from local supermarkets, found higher levels of omega-3 fats and a more health-beneficial ratio of omega-6 to omega-3 fats. Despite small sample sizes, all three crop comparisons show differences in micronutrient and phytochemical concentrations that suggest soil health is an under appreciated influence on nutrient density, particularly for phytochemicals not conventionally considered nutrients but nonetheless relevant to chronic disease prevention. Likewise, regenerative grazing practices produced meat with a better fatty acid profile than conventional and regional health-promoting brands. Together these comparisons offer preliminary support for the conclusion that regenerative soil-building farming practices can enhance the nutritional profile of conventionally grown plant and animal foods.
Montgomery et al. (2022) Soil health and nutrient density: preliminary comparison of regenerative and conventional farming. PeerJ 10:e12848 https://doi.org/10.7717/peerj.12848
Effects of inorganic mercury exposure in the alveolar bone of rats: an approach of qualitative and morphological aspects
Background In comparison to organic mercury (MeHg), the environmental inorganic mercury (IHg) can be found in some skin-lightening cosmestics were considered “harmless” for a long time. However, recent studies have shown that long-term exposure to low doses of IHg may affect biological systems. Therefore, this study investigated the effects of IHg long-term exposure to the alveolar bone of adult rats. Methods Adult Wistar rats were distributed in control and HgCl2 exposed (0.375 mg/kg/day). After 45 days, the rats were euthanized and both blood and hemimandibles were collected. Total blood Hg levels were measured and both inorganic and organic components of the alveolar bone were determined through XRD and ATR-FTIR. The microstructure of the alveolar bone was assessed by using micro-CT and the morphometric analysis was performed by using stereomicroscopy. Results Alterations in the physicochemical components of the alveolar bone of exposed animals were observed. The bone changes represented a tissue reaction at the microstructural level, such as bone volume increase. However, no significant dimensional changes (bone height) were observed. Conclusion Exposure to IHg at this dose can promote microstructural changes and alteration in the organic and inorganic components in the alveolar bone.
Nunes et al. (2022) Effects of inorganic mercury exposure in the alveolar bone of rats: an approach of qualitative and morphological aspects. PeerJ 10:e12573 https://doi.org/10.7717/peerj.12573
miR-148a-3p inhibits the proliferation and migration of bladder cancer via regulating the expression of ROCK-1
Purpose To investigate the mechanism of miR-148a-3p regulating the proliferation and migration of bladder tumor cells. Materials and Methods We conducted a preliminary study to detect the relative expression of miR-148a-3p in bladder cancer and para-cancerous tissue samples. Three bladder tumor cell lines, T24, 5,637 and UM-UC-3, were selected. The expression levels of miR-148a-3p were artificially regulated with miR-148a-3p mimics and the miR-148a-3p inhibitor. The relative expression levels of miR-148a-3p in the samples of each cell line were determined. Cell Counting Kit-8 (CCK-8) was used to detect cell proliferation, while the effect of the miR-148a-3p mimics and inhibitor on tumor cell migration was detected by wound healing assay. Flow cytometry assay was carried out to explore the effect of miR-148a-3p on cell apoptosis. Dual-luciferase reporter assay was performed in order to verify miR-148a-3p’s target gene. The expressions of ROCK-1 and Bcl-2 were analyzed by western blot. Results The relative expression of miR-148a-3p in tumor and adjacent tissues was assessed with qRT-PCR (P < 0.05) and found to be significantly lower in the tumor tissues than the adjacent tissues. The data obtained from the CCK-8 and wound healing assay showed that intracellular transfection of miR-148a-3p mimics could inhibit cell proliferation and migration, while the miR-148a-3p inhibitor promoted them. Overexpression of miR-148a-3p promoted cell apoptosis in the T24 and 5,637 cell lines. The dual-luciferase reporter assay verified that ROCK-1 is a direct target of miR-148a-3p. Western blot showed that miR-148a-3p overexpression downregulated the expression of ROCK-1 and Bcl-2, while miR-148a-3p knockdown upregulated the expression of ROCK-1 and Bcl-2. Conclusions We confirmed that miR-148a-3p was significantly decreased in bladder cancer cells. miR-148a-3p overexpression inhibited bladder cancer cell proliferation and migration, whereas miR-148a-3p knockdown promoted bladder cancer cell proliferation and migration. Moreover, we found that ROCK-1 was a downstream target of miR-148a-3p. We also found that miR-148a-3p induced cell apoptosis by regulating the expression of Bcl-2. However, the deeper mechanism of this regulatory relationship needs further study.
Xu et al. (2022) miR-148a-3p inhibits the proliferation and migration of bladder cancer via regulating the expression of ROCK-1. PeerJ 10:e12724 https://doi.org/10.7717/peerj.12724
The performance of body mass component indices in detecting risk of musculoskeletal injuries in physically active young men and women
Background Body composition indices can be related to musculoskeletal injuries (MI), particularly in physically active groups. However, little is known about the accuracy of these diagnoses as potential predictors of musculoskeletal injuries. Therefore, this study aims to indicate the cut-off points of relative body mass (BMI), fat mass index (FMI), skeletal muscle mass (SMI), and muscle to fat ratio (MFR) and establish its reliability in injury prediction for physically active men and women. Methods The sample included 119 physically active individuals aged 23.72 ± 1.12 (66 men body height 1.79 ± 0.07 (m); body weight 80.51 ± 9.85 (kg) and 53 women body height 1.67 ± 0.08 (m); body weight 62 ± 10.72 (kg)), students at university of physical education in Poland. The participants’ physical activity was measured with the International Physical Activity Questionnaire (IPAQ). The relevance of body mass index (BMI), fat mass index (FMI), skeletal muscle mass index (SMI), and muscle to fat ratio (MFR) in detecting injury risk was examined. Musculoskeletal injuries during 1 year before examination were registered using a self-reporting questionnaire. The areas under the curve (AUC) and Youden Index in the receiver operating characteristic curve (ROC) were calculated. Results The cut-off points used to classify the indices among men were BMI = 24.38; FMI = 3.74; SMI = 16.40; MFR = 3.70; and for women BMI = 20.90; FMI = 4.17; SMI = 8.96; MFR = 1.67. Results suggested the greatest reliability in the prediction of musculoskeletal injuries among men had BMI (AUC = 0.623; Youden = 0.30) and SMI (AUC = 0.608; Youden = 0.23) whereas among women, MFR (AUC = 0.628; Youden = 0.29) and FMI (AUC = 0.614; Youden = 0.32). Conclusion BMI and SMI are the most appropriate indices to predict the risk of musculoskeletal injury in physically active men, whereas in women, MFR and FMI are more reliable. These results indicate that the indices with more muscle mass meaning are better in predicting injury among men. In contrast, indices with a higher contribution of fat are better for women. It indicates sex differentiation of injury risk conditions. Men should focus on developing muscle mass, whereas women should reduce body fat to decrease injury risk. However, widespread use seemed to be limited to the specific examined group. Therefore, cut-off points should be used with caution, and calculated values should be verified and confirmed in subsequent studies.
Domaradzki et al. (2022) The performance of body mass component indices in detecting risk of musculoskeletal injuries in physically active young men and women. PeerJ 10:e12745 https://doi.org/10.7717/peerj.12745
Comparison of the bleaching susceptibility of coral species by using minimal samples of live corals
In massive bleaching events (losing symbiotic algae from corals), more sensitive corals are bleached earlier than other corals. To perform a comparison of bleaching susceptibility within and across coral species, a simple quantitative method is required. Accordingly, we present a laboratory-based method for comparing the bleaching susceptibility of various coral species by using a standardized image analysis protocol. Coral fragments were sampled from the colonies of five species selected from Kenting, southern Taiwan, and maintained in the same aquarium tank with circulating seawater; 2 seawater temperature regimes were used (i.e., fast-heating program (FHP), with a heating rate of 1 °C per day; and slow-heating program (SHP), with a heating rate of 1 °C per 3 days). Each coral fragment was photographed periodically, and the colored images were subsequently converted to grayscale images and then digitally analyzed to determine the standardized grayscale values (G0) by comparing with that of standard color strip. The G0 of a sample at each time of photographing during bleaching was divided by the difference of G0 between the acclimating and the same but completely bleached fragment to derive the relative grayscale (RG%) at a particular stage of bleaching; this is done for each coral fragment of a colony. The smaller the RG% of a coral fragment the closer it is approaching completely bleached condition. The level of decrease in RG% within a time series of images in each heating regime was used to establish a bleaching time index (BTI). The lower the BTI, the sooner to reach a defined bleaching level (e.g., 30%), this indicates the coral is more sensitive to thermal bleaching. In the experiment, we compared the bleaching susceptibility of the five species. Based on the proposed BTI, the five species were ranked in terms of bleaching susceptibility, and the rankings were identical between the two temperature regimes; three species in Pocilloporidae had lower BTI, whereas the hydrocoral Millepora species had the highest BTI. Within each heating regime, the BTI of different species were ranked and used to indicate susceptibility. In the FHP, the three Pocilloporidae species could be divided into two groups in terms of bleaching susceptibility. FHP not only displayed a higher differentiating capability on coal bleaching susceptibility than SHP, but also had a faster completion time, thus reducing the likelihood of unforeseen complications during the tank experiments. Our color-based method is easier and less effort-intensive than methods involving the assessment of zooxanthellae densities. Moreover, it requires much fewer replicates and all samples in one large tank (e.g., 300 L) for the studies considering multiple species comparisons. This method opens opportunities for studying the effects of species types, acclimatization (e.g., seasons), and environmental factors other than temperature on coral bleaching.
Wang et al. (2022) Comparison of the bleaching susceptibility of coral species by using minimal samples of live corals. PeerJ 10:e12840 https://doi.org/10.7717/peerj.12840
Potential impacts from simulated vessel noise and sonar on commercially important invertebrates
Human usage of coastal water bodies continues to increase and many invertebrates face a broad suite of anthropogenic stressors (e.g., warming, pollution, acidification, fishing pressure). Underwater sound is a stressor that continues to increase in coastal areas, but the potential impact on invertebrates is not well understood. In addition to masking natural sound cues which may be important for behavioral interactions, there is a small but increasing body of scientific literature indicating sublethal physiological stress may occur in invertebrates exposed to high levels of underwater sound, particularly low frequency sounds such as vessel traffic, construction noise, and some types of sonar. Juvenile and sub-adult blue crabs (Callinectes sapidus) and American lobsters (Homarus americanus) were exposed to simulated low-frequency vessel noise (a signal was low-pass filtered below 1 kHz to ensure low-frequency content only) and mid-frequency sonar (a 1-s 1.67 kHz continuous wave pulse followed by a 2.5 to 4.0 kHz 1-s linear frequency modulated chirp) and behavioral response (the animal’s activity level) was quantified during and after exposure using EthoVision XT™ from overhead video recordings. Source noise was quantified by particle acceleration and pressure. Physiological response to the insults (stress and recovery) were also quantified by measuring changes in hemolymph heat shock protein (HSP27) and glucose over 7 days post-exposure. In general, physiological indicators returned to baseline levels within approximately 48 h, and no observable difference in mortality between treatment and control animals was detected. However, there was a consistent amplified hemolymph glucose signal present 7 days after exposure for those animals exposed to mid-frequency sound and there were changes to C. sapidus competitive behavior within 24 h of exposure to sound. These results stress the importance of considering the impacts of underwater sound among the suite of stressors facing marine and estuarine invertebrates, and in the discussion of management actions such as protected areas, impact assessments, and marine spatial planning efforts.
Hudson et al. (2022) Potential impacts from simulated vessel noise and sonar on commercially important invertebrates. PeerJ 10:e12841 https://doi.org/10.7717/peerj.12841
Isolation, identification and characterization of nitrogen fixing endophytic bacteria and their effects on cassava production
Background Cassava (Manibot esculenta Crantz) is one of the most important among tuber crops. The amount of nitrogen fertilizer used for cassava production is relatively high (400 kg ha−1), but there are few studies on biological nitrogen fixation in this crop. Therefore, it is particularly important to study whether cassava and microorganisms have the associated nitrogen-fixing and other promoting effects of endophytic bacteria. Methods We screened 10 endophytic bacteria using the nitrogen-free culture method from the roots of seven cassava cultivars, and the nitrogenase activity of the A02 strain was the highest 95.81 nmol mL−1 h−1. The A02 strain was confirmed as Microbacteriaceae, Curtobacterium using 16S rRNA sequence alignment. The biological and morphological characteristics of strain A02 were further analyzed. Results The experimental results showed that the biomass of roots, stems, and leaves of cassava inoculated with A02 increased by 17.6%, 12.6%, and 10.3%, respectively, compared to that of the control (without A02 inoculation). These results were not only related to the secretion of auxin (IAA) and solubilization of phosphate but also in the promotion of biological nitrogen fixation of cassava leaves by strain A02. Moreover, the highest 95.81 nmol mL−1h−1 of nitrogenase activity was reported in strain A02, and thus more nitrogen fixation was observed in strain A02. In conclusion, A02 is a newly discovered endophytic nitrogen-fixing bacteria in cassava that can be further used in the research of biological bacterial fertilizers.
Zhang et al. (2022) Isolation, identification and characterization of nitrogen fixing endophytic bacteria and their effects on cassava production. PeerJ 10:e12677 https://doi.org/10.7717/peerj.12677
Diversity and structure of the microbial community in rhizosphere soil of Fritillaria ussuriensis at different health levels
Fritillaria wilt is a kind of soil-borne disease that causes a large reduction in the yield of Fritillaria ussuriensis. The diversity and structure of the soil microbial community are important factors affecting the health of Fritillaria ussuriensis. The analysis of the microbial community in the diseased and healthy soils provided a theoretical basis for revealing the pathological mechanism and prevention of Fritillaria wilt disease. In the present study, we sequenced the soil microorganisms from healthy (H), pathology (P) and blank (B) soil samples by Illumina MiSeq. Determined the soil physicochemical properties respectively, analyzed the soil microbial diversity and structure, and constructed single factor co-correlation networks among microbial genera. The results showed that Ascomycota (48.36%), Mortierellomycota (23.06%), Basidiomycota (19.00%), Proteobacteria (31.74%), and Acidobacteria (20.95%) were dominant in the soil. The diversity of healthy soil was significantly greater than that of diseased soil samples (P and B) (P < 0.05). The populations of Fusarium and Humicola significantly increased in the diseased soil sample (P and B) (P < 0.05). RB41 (4.74%) and Arthrobacter (3.30%) were the most abundant genera in the healthy soil. Total nitrogen (TN), available nitrogen (AN), total potassium (TK), available potassium (AK), and inorganic salt (salt) were significantly correlated with soil microbial communities (P < 0.05). The relationship between fungi and the plant was mostly positive, whereas bacteria showed the opposite trend. In conclusion, the diversity and structure of the soil microbial community were closely related to the health level of Fritillaria ussuriensis. Fusarium and Humicola affect the severity of Fritillaria wilt disease, while RB41 and Arthrobacter are the important indicators for maintaining the health of Fritillaria ussuriensis. Moreover, environmental factors greatly affect the abundance and formation of soil microbial community. The interactions in microbial communities also influence the healthy growth of Fritillaria ussuriensis.
Jiao et al. (2022) Diversity and structure of the microbial community in rhizosphere soil of Fritillaria ussuriensis at different health levels. PeerJ 10:e12778 https://doi.org/10.7717/peerj.12778